To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")
In most cases, you don't need to download the package archive at all.
mzR
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parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Bioconductor version: Release (3.5)
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
Maintainer: Bernd Fischer <b.fischer at dkfz.de>, Steffen Neumann <sneumann at ipb-halle.de>, Laurent Gatto <lg390 at cam.ac.uk>, Qiang Kou <qkou at umail.iu.edu>
Citation (from within R,
enter citation("mzR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mzR")
| R Script | Accessin raw mass spectrometry and identification data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 2.10.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (6 years) |
| License | Artistic-2.0 |
| Depends | Rcpp (>= 0.10.1), methods, utils |
| Imports | Biobase, BiocGenerics(>= 0.13.6), ProtGenerics |
| LinkingTo | Rcpp, zlibbioc |
| Suggests | msdata(>= 0.15.1), RUnit, mzID, BiocStyle, knitr, XML |
| SystemRequirements | C++11, GNU make, NetCDF |
| Enhances | |
| URL | https://github.com/sneumann/mzR/ |
| BugReports | https://github.com/sneumann/mzR/issues/ |
| Depends On Me | MSGFgui, MSnbase |
| Imports Me | MSnID, msPurity, Pbase, ProteomicsAnnotationHubData, RMassBank, SIMAT, xcms, yamss |
| Suggests Me | AnnotationHub, msdata, qcmetrics, RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mzR_2.10.0.tar.gz |
| Windows Binary | mzR_2.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | mzR_2.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mzR |
| Package Short Url | http://bioconductor.org/packages/mzR/ |
| Package Downloads Report | Download Stats |
Documentation »
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